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- RNAi & Custom RNA Synthesis
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siRNA FAQs
1. Can Customer Service representatives see my Gene Cart in the same way they can see my shopping cart?
The Gene Cart contents do not appear in our internal systems in the same way as the shopping cart. A Gene Cart is, however, perpetuated in the same way as your shopping cart. If you are logged in with a valid Dharmacon account, or continue an anonymous session without deleting cookies, the Gene Cart will be available during subsequent sessions.
2. Can I create multiple gene carts? Can I email them to someone?
That functionality is not available at this time, but we are hoping to expand the utility of the Gene Cart with future releases.
3. Can I build a Gene Cart and order the Cherry-pick Library at a later time?
A Gene Cart is perpetuated in the same way as your shopping cart. If you are logged in with a valid Dharmacon account, or continue an anonymous session without deleting cookies, the Gene Cart will be available during subsequent sessions.
4. Can I export my gene cart?
Export functionality is not available from the Gene Cart. Our instance of Ingenuity is for the support of gene-based products, not as a standalone bioinformatics tool. A full suite of tools to utilize the Ingenuity annotations and functionality are available via licensing of the Ingenuity Pathway Analysis tool (IPA) at
5. Why are there so many items with “No results”when I send my cart contents to the Cherry-pick Plater?
The Gene Cart will accept items from Ingenuity that may be part of a pathway or interaction that are not valid when mapping them to specific Human or Mouse gene-based siRNA and microRNA products (genes assigned to other species, drugs, gene families, etc.). You can control the types of molecules added to the Gene Cart by using the Filter or Highlight checkboxes within the Ingenuity views (Interaction Net and Biological Pathways
6. What is the Dicer cleavage site for shRNAmir hairpins?
The Dicer cleavage site is at the 11th base from the 5' end of the shRNA hairpin (antisense).
7. What is the difference between siGENOME and ON-TARGETplus siRNA?
The Dharmacon siGENOME collection of pre-designed siRNA are the most cited siRNA in the world, and have been trusted for superior silencing since 2002. These siRNAs are, for the most part, unmodified and are a reliable choice for every gene silencing application. The ON-TARGETplus collection takes advantage of a dual-strand modification pattern to decrease off-target effects by up to 90%. Both the siGENOME and the ON-TARGETplus products carry the same functional guarantee - 75% silencing or better by the SMARTpool and at least three of the four individuals. We do encourage new research projects and new customers to begin with the ON-TARGETplus platform to have the advantage of the performance-enhancing modifications. The siGENOME products are available for ongoing experiments and for studies which require the use of unmodified siRNAs.
8. Can I order shRNA or ORFs based on my Gene Cart entries?
At this time the Gene Cart only supports automatic ordering of siRNA and microRNA reagents via the Cherry-pick Library Plater. Please contact Technical Support for assistance on ordering vector-based products based on a gene list.
9. Do you have pre-designed siRNAs against my gene of interest?
We have pre-designed siRNAs for nearly all human, mouse, and rat protein-coding genes in the RefSeq database. To find pre-designed siRNAs for your gene of interest, first initiate a search for your gene on You can use the gene name, gene symbol, gene ID, or RefSeq accession number as a search term. Once your search results are displayed, click on the desired gene to view a list of products available for that target. You are encouraged review the detailed gene information at the top of the page and use the gene ID link to view the NCBI Entrez Gene page if necessary to confirm that you have identified the correct target gene.
10. Which transfection reagent should I use with my specific cell line?
The best transfection reagent for your experiments will depend on the cell line that you are using, and must be determined empirically. Dharmacon has available four different lipid-based transfection reagents that have been specially formulated for delivery of siRNAs into cells. These DharmaFECT transfection reagents are very mild yet have very high transfection rates into a wide variety of cell lines. Please consult the Resource Library on for optimized conditions and transfection protocols. If your cell line is not identified in the compatibility table ( and you are not able to find an example of siRNA delivery in this cell line in published literature, we recommend testing multiple reagents to identify the best one for your experiments. The best transfection reagent is one that results in a high level of siRNA delivery with a low level of cell toxicity. The best method for confirming siRNA delivery is to assay knockdown, preferably at the mRNA level, by a positive control siRNA that targets a housekeeping gene for which silencing is well characterized."
11.What are the most important controls for my siRNA experiment?
A non-targeting siRNA control is designed to have no known target in the cells being used. These negative controls are important for distinguishing sequence-specific silencing from non-specific effects in the RNAi experiment. Because non-specific effects can be siRNA concentration dependent, it is important to use negative control siRNA at the same concentration as your gene-specific siRNA. Efficient delivery of siRNA is critical for achieving significant gene silencing. A positive control siRNA can be used to optimize delivery conditions and to monitor transfection efficiency throughout your experiments. An extensively validated siRNA that targets a housekeeping gene is ideal as a positive control. We offer several positive and negative controls in our Accell, ON-TARGETplus, and siGENOME product lines as well as fluorescent controls for your siRNA experiments. Please refer to our Technical Note: Effective Controls for RNAi Experiments to learn more
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12. How should I resuspend my siRNA?
Your siRNA can be resuspended in any RNase-free buffer or RNase-free water. For convenience we do offer a 5X siRNA Buffer (B-002000-UB-100) and RNase-free water (B-002000-WB-100) for purchase separately. We recommend following the Basic siRNA Resuspension protocol ( to ensure complete resuspension of the pellet.
13. Do you have siRNA for in vivo experiments?
There are two things to consider when using siRNA in animal models: siRNA stability and toxicity to the animal. We offer a proprietary modification to address stability and in vivo processing options to address potential toxicity, both of which can be selected for any custom siRNA synthesis. The method of delivery used in the experiment will determine whether one or both of these options is recommended. The siSTABLE™modification pattern dramatically enhances siRNA stability in nuclease-rich environments resulting in the siRNA reaching the target tissue to enable gene silencing. This modification is typically used for systemic injections into the blood stream, topical applications, and other applications where the siRNA is not protected by a carrier from nuclease degradation. The in vivo and in vivo HPLC processing options for custom siRNA both include counter ion (Na+) exchange, desalting, sterile filtration, and endotoxin testing. Additionally, an in vivo HPLC processed duplex has undergone ion exchange HPLC purification. Finally, the siRNA is lyophilized to allow greater solubility under the higher concentrations typically used for in vivo injections.
14. Which human lncRNAs do your Lincode siRNAs target?
Lincode siRNA reagents target human non-coding RNA genes in the RefSeq v.54 database that meet the following criteria: 1.)Greater than or equal to 200 nt in length 2.)The gene record contains at least one RefSeq Accession prefix of NR_ or XR_ 3.)The record is designated as lncRNA or miscellaneous RNA. Genes characterized as tRNA, rRNA, snoRNA, miRNA, etc. are excluded from these product lines
15. Do you have siRNA for my gene of interest? How do I find it?
We have siRNA for most human, mouse and rat genes. To find siRNA for your gene, first search for your gene (using a gene name, gene ID or gene accession number) using the search tool bar, and then click on the “siRNA”hyperlink on the right hand side of your intended gene description in the “Genes”results field.
16. What is the difference between ON-TARGETplus, siGENOME and Accell siRNA?
siGENOME is our original siRNA product. ON-TARGETplus siRNA reagents deliver the highest-confidence RNAi results available by combining guaranteed silencing with unmatched strategies for greater target specificity. Accell is the only siRNA modified for delivery into difficult-to-transfect cells.
17. What advantages do your Lincode products offer?
1.SMARTpool format: When you consider the potential for inaccessible or unrecognized siRNA recognition sites (tertiary structure, DNA- or protein bound, variability in sequence record etc.), the SMARTpool provides increased likelihood that a.one of the four siRNAs will access its target site b.that the functional domain of the RNA will be degraded 2.ON-TARGETplus modifications: preventing off-targets is just as important in lncRNA experiments as in other gene knockdown (if not more so). a.Passenger (sense) strand blocking: The siRNA sense strand could have 100% homology to an opposite-strand protein coding transcript, or could target other genes. b.Guide (antisense) strand seed region: As with any siRNA, the seed region can act like a microRNA by inducing off-targets. Since the effects of lncRNA knockdown can be very subtle, it is more important than ever to reduce off-targets that could confound interpretation of the phenotype.
18. What is guarantee for the Lincode siRNAs?
mRNAs are required to be accessible to translation machinery, and therefore accessible to RNAi as well. This is not true for lncRNAs. The ability to detect them (e.g. via NGS) does not give indication that they can be knocked down. We cannot ensure that the target is expressed and accessible to RISC machinery, which would make the siRNA appear non-functional when in fact it is an issue of the biology around the intended target. a. Nuclear localization b. DNA- or protein-bound RNA target c. Secondary structure Due to this biology, we do not guarantee the function of these reagents
19. I want to silence lncRNAs that you don’t have products for. What should I do?
To design and order siRNAs targeting lncRNA that fall outside of the Lincode pre-designed products, follow these steps: 1.Go to the siDESIGN Center ( and enter the RefSeq ID or nucleotide sequence of the lncRNA you wish to target 2.Select the BLAST database that includes NM and NR (coding and non-coding transcripts) for your species of interest 3.Add desired designs to your cart, then click each item to select ON-TARGETplus modifications to ensure strand-specific silencing
20. What is the average molecular weight of an siRNA?
The average molecular weight of a 21 mer siRNA duplex is 13,300 g/mol. Therefore, 1 nmol siRNA = 13.3 micrograms of siRNA, or 1 mg siRNA = 75 nmol.
21.What stock concentration is recommended for pre-designed siRNAs?
Pre-designed siRNAs are shipped as a dried pellet and are ready for resuspension in an appropriately buffered, RNase-free solution. We recommend stock concentrations between 20 - 100 uM, depending upon the initial quantity of siRNA supplied. For example, a 5 nmol quantity resuspended in 250 uL of buffer will result in a 20 uM stock solution. Alternatively, a 50 nmol quantity resuspended in 1 mL of buffer will result in a 50 uM stock solution. Please reference the FAQ under Calculations for information about how to calculate a specific stock concentration.
22. Which pre-designed siRNA product line should I select, ON-TARGETplus or siGENOME?
We do encourage new research projects and new customers to begin with the ON-TARGETplus platform to have the advantage of the performance-enhancing modifications. The siGENOME products are still available for ongoing experiments and for studies which require the use of unmodified siRNAs.
23. Can I use Dharmacon siRNA reagents in an in vivo system?
Dharmacon offers an in vivo processing option designed for siRNAs in animal models. siRNAs synthesized by 2' ACE synthesis chemistry have an amine counterion present during synthesis; therefore, we recommend and offer a salt exchange to the sodium counterion followed by dialysis to remove excess salt ions in the preparation of siRNAs intended for use in animals. Read more here about these processing options.
24. Should I use polypropylene or polystyrene plates to store my library (siRNA, miRNA, shRNA, cDNA, ORF)?
There is a trade-off between polypropylene and polystyrene for storage at -80C. With polypropylene, the plates can warp making use with automated/robotics systems problematic. With polystyrene, the plate can be very brittle while frozen at such a low temperature, but the problem is not permanent - once the plate is thawed it is not as brittle any longer. So you must decide which features are more important to you. We tend to use polystyrene for most things as it is more conducive to our automated manufacturing environment. For synthetic siRNA and miRNA libraries, a storage temperature of -20C can be used to minimize the problems associated with storage of plates at lower temperatures.
25. What is a SMARTpool siRNA reagent?
The SMARTpool siRNA reagent is a pool of four siRNA duplexes all designed to target distinct sites within the specific gene of interest. The siRNA sequences are selected using Dharmacon's SMARTselection design algorithm and then analyzed for significant sequence identity with other non-targeted genes using a unique, modified BLAST analysis against a curated database for the appropriate species.